Atomistry » Calcium » PDB 3hjb-3hz3 » 3hx4
Atomistry »
  Calcium »
    PDB 3hjb-3hz3 »
      3hx4 »

Calcium in PDB 3hx4: Crystal Structure of CDPK1 of Toxoplasma Gondii, TGME49_101440, in Presence of Calcium

Protein crystallography data

The structure of Crystal Structure of CDPK1 of Toxoplasma Gondii, TGME49_101440, in Presence of Calcium, PDB code: 3hx4 was solved by A.K.Wernimont, J.D.Artz, P.Finnerty, T.Xiao, H.He, F.Mackenzie, G.Sinestera, A.A.Hassani, G.Wasney, M.Vedadi, S.Lourido, A.Bochkarev, C.H.Arrowsmith, A.M.Edwards, C.Bountra, J.Weigelt, D.L.Sibley, R.Hui, Y.H.Lin, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.236, 95.605, 101.612, 90.00, 90.00, 90.00
R / Rfree (%) 20.9 / 25.7

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of CDPK1 of Toxoplasma Gondii, TGME49_101440, in Presence of Calcium (pdb code 3hx4). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of CDPK1 of Toxoplasma Gondii, TGME49_101440, in Presence of Calcium, PDB code: 3hx4:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3hx4

Go back to Calcium Binding Sites List in 3hx4
Calcium binding site 1 out of 4 in the Crystal Structure of CDPK1 of Toxoplasma Gondii, TGME49_101440, in Presence of Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of CDPK1 of Toxoplasma Gondii, TGME49_101440, in Presence of Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca601

b:32.0
occ:1.00
O A:TYR421 2.3 21.1 1.0
OD1 A:ASP415 2.3 26.1 1.0
OD1 A:ASP417 2.3 25.6 1.0
OE2 A:GLU423 2.4 27.2 1.0
OE1 A:GLU426 2.4 21.4 1.0
OD1 A:ASN419 2.4 20.3 1.0
OE2 A:GLU426 2.6 22.3 1.0
CD A:GLU426 2.9 22.2 1.0
CG A:ASN419 3.4 22.7 1.0
CG A:ASP415 3.4 26.5 1.0
CD A:GLU423 3.5 29.2 1.0
CG A:ASP417 3.5 26.7 1.0
C A:TYR421 3.5 20.7 1.0
OE1 A:GLU423 3.9 29.4 1.0
ND2 A:ASN419 4.0 21.0 1.0
OD2 A:ASP417 4.0 26.7 1.0
OD2 A:ASP415 4.1 25.9 1.0
N A:ASN419 4.3 23.6 1.0
CA A:ASP415 4.3 26.9 1.0
N A:TYR421 4.3 21.9 1.0
N A:GLU423 4.3 20.3 1.0
N A:ASP417 4.3 26.1 1.0
CG A:GLU426 4.3 21.3 1.0
CB A:ASP415 4.4 26.4 1.0
N A:ILE422 4.4 20.5 1.0
CA A:ILE422 4.4 20.3 1.0
CB A:ASN419 4.4 22.9 1.0
CA A:TYR421 4.4 21.0 1.0
C A:ASP415 4.5 26.5 1.0
N A:PHE416 4.6 26.7 1.0
N A:LYS418 4.7 25.3 1.0
CB A:ASP417 4.7 26.0 1.0
CG A:GLU423 4.7 24.6 1.0
CA A:ASN419 4.7 23.3 1.0
CB A:GLU423 4.8 21.5 1.0
C A:ILE422 4.8 20.6 1.0
CB A:TYR421 4.8 20.6 1.0
CA A:ASP417 4.8 26.2 1.0
N A:GLY420 4.9 22.9 1.0
C A:ASP417 4.9 25.8 1.0
O A:HOH541 4.9 16.7 1.0

Calcium binding site 2 out of 4 in 3hx4

Go back to Calcium Binding Sites List in 3hx4
Calcium binding site 2 out of 4 in the Crystal Structure of CDPK1 of Toxoplasma Gondii, TGME49_101440, in Presence of Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of CDPK1 of Toxoplasma Gondii, TGME49_101440, in Presence of Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca602

b:31.9
occ:1.00
OD1 A:ASP368 2.2 24.3 1.0
O A:HOH508 2.2 21.4 1.0
O A:GLN374 2.3 25.3 1.0
OD1 A:ASN370 2.3 22.1 1.0
OE1 A:GLU379 2.4 21.6 1.0
OD2 A:ASP372 2.4 19.5 1.0
OE2 A:GLU379 2.5 19.1 1.0
CD A:GLU379 2.8 21.3 1.0
CG A:ASN370 3.4 23.7 1.0
CG A:ASP372 3.4 22.1 1.0
CG A:ASP368 3.4 23.3 1.0
C A:GLN374 3.5 25.7 1.0
OD1 A:ASP372 3.8 22.7 1.0
ND2 A:ASN370 3.8 21.9 1.0
N A:GLN374 4.1 26.2 1.0
OD2 A:ASP368 4.2 23.0 1.0
N A:ASP372 4.2 22.1 1.0
CG A:GLU379 4.3 22.4 1.0
CA A:GLN374 4.3 26.2 1.0
CA A:ASP368 4.4 23.0 1.0
CB A:ASP368 4.4 22.9 1.0
N A:ASN370 4.4 23.4 1.0
N A:LEU375 4.4 24.6 1.0
CA A:LEU375 4.4 24.1 1.0
N A:GLY371 4.5 23.2 1.0
C A:ASP368 4.5 23.1 1.0
CB A:ASP372 4.6 22.6 1.0
N A:ASP376 4.6 23.8 1.0
CB A:GLN374 4.6 26.9 1.0
CB A:ASN370 4.6 23.2 1.0
N A:GLY373 4.7 24.0 1.0
N A:LYS369 4.7 23.4 1.0
OD2 A:ASP376 4.8 25.8 1.0
CA A:ASP372 4.8 22.8 1.0
CA A:ASN370 4.8 23.6 1.0
C A:ASN370 4.9 23.5 1.0
C A:ASP372 4.9 23.2 1.0
C A:LEU375 5.0 24.4 1.0
CG A:ASP376 5.0 24.4 1.0
O A:ASP368 5.0 22.3 1.0

Calcium binding site 3 out of 4 in 3hx4

Go back to Calcium Binding Sites List in 3hx4
Calcium binding site 3 out of 4 in the Crystal Structure of CDPK1 of Toxoplasma Gondii, TGME49_101440, in Presence of Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of CDPK1 of Toxoplasma Gondii, TGME49_101440, in Presence of Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca603

b:47.7
occ:1.00
O A:HOH587 2.2 25.5 1.0
OD1 A:ASP451 2.2 23.0 1.0
O A:LYS457 2.3 24.3 1.0
OD2 A:ASP453 2.4 28.0 1.0
OG A:SER455 2.5 25.3 1.0
OE2 A:GLU462 2.6 27.9 1.0
OE1 A:GLU462 2.7 25.1 1.0
CD A:GLU462 3.0 26.3 1.0
CG A:ASP451 3.4 23.8 1.0
CG A:ASP453 3.5 27.5 1.0
C A:LYS457 3.5 24.1 1.0
CB A:SER455 3.6 26.7 1.0
OD1 A:ASP453 3.9 26.6 1.0
N A:SER455 3.9 26.9 1.0
N A:LYS457 4.1 24.4 1.0
CA A:ASP451 4.2 24.9 1.0
CA A:SER455 4.3 26.4 1.0
OD2 A:ASP451 4.3 21.9 1.0
CB A:ASP451 4.3 24.2 1.0
N A:ILE458 4.4 23.6 1.0
CA A:LYS457 4.4 24.2 1.0
C A:ASP451 4.4 24.9 1.0
CA A:ILE458 4.4 23.0 1.0
N A:ASP453 4.5 26.6 1.0
CG A:GLU462 4.5 25.5 1.0
N A:ASN454 4.6 27.3 1.0
N A:SER452 4.6 25.6 1.0
N A:GLY456 4.6 25.7 1.0
CB A:ASP453 4.7 26.8 1.0
N A:SER459 4.8 22.6 1.0
C A:SER455 4.8 26.2 1.0
C A:ASP453 4.8 26.9 1.0
CA A:ASP453 4.9 26.9 1.0
O A:ASP451 4.9 25.1 1.0
C A:ASN454 5.0 27.3 1.0

Calcium binding site 4 out of 4 in 3hx4

Go back to Calcium Binding Sites List in 3hx4
Calcium binding site 4 out of 4 in the Crystal Structure of CDPK1 of Toxoplasma Gondii, TGME49_101440, in Presence of Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of CDPK1 of Toxoplasma Gondii, TGME49_101440, in Presence of Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca604

b:49.2
occ:1.00
O A:HOH588 2.2 19.8 1.0
O A:GLU491 2.4 24.6 1.0
OD2 A:ASP485 2.4 27.7 1.0
OD1 A:ASN487 2.4 24.5 1.0
OE1 A:GLU496 2.5 26.0 1.0
OE2 A:GLU496 2.6 25.4 1.0
OD1 A:ASP489 2.6 26.5 1.0
CD A:GLU496 2.9 24.9 1.0
CG A:ASP489 3.3 26.7 1.0
CG A:ASP485 3.6 26.9 1.0
C A:GLU491 3.6 24.6 1.0
OD2 A:ASP489 3.6 27.2 1.0
CG A:ASN487 3.6 27.0 1.0
OD2 A:ASP493 4.2 26.2 1.0
ND2 A:ASN487 4.2 26.8 1.0
N A:GLU491 4.2 24.5 1.0
N A:ASP489 4.3 26.0 1.0
OD1 A:ASP485 4.3 26.2 1.0
CA A:ASP485 4.3 27.3 1.0
CG A:GLU496 4.4 24.6 1.0
N A:VAL492 4.5 24.4 1.0
CA A:VAL492 4.5 24.0 1.0
N A:ASN487 4.5 27.0 1.0
CA A:GLU491 4.5 25.0 1.0
CB A:ASP485 4.5 27.2 1.0
N A:ASP493 4.5 24.6 1.0
CB A:ASP489 4.6 25.9 1.0
N A:ASN488 4.6 26.3 1.0
C A:ASP485 4.7 27.4 1.0
N A:LYS486 4.7 27.4 1.0
CB A:ASN487 4.7 26.8 1.0
N A:GLY490 4.8 25.2 1.0
CA A:ASP489 4.8 25.8 1.0
C A:ASN487 4.8 26.6 1.0
CG A:ASP493 4.8 25.6 1.0
CA A:ASN487 4.9 26.9 1.0

Reference:

A.K.Wernimont, J.D.Artz, P.Finerty, Y.H.Lin, M.Amani, A.Allali-Hassani, G.Senisterra, M.Vedadi, W.Tempel, F.Mackenzie, I.Chau, S.Lourido, L.D.Sibley, R.Hui. Structures of Apicomplexan Calcium-Dependent Protein Kinases Reveal Mechanism of Activation By Calcium. Nat.Struct.Mol.Biol. V. 17 596 2010.
ISSN: ISSN 1545-9993
PubMed: 20436473
DOI: 10.1038/NSMB.1795
Page generated: Sat Jul 13 11:12:52 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy